Contacts of the helix formed by residues 19 - 33 (chain B) in PDB entry 4Q96
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 2.8 8.5 + - - -
18B ASN* 1.3 78.9 - - - +
20B GLN* 1.3 62.4 + - - +
21B HIS* 3.5 10.0 + - - +
22B SER* 2.8 27.4 + - - -
23B VAL* 3.0 23.0 + - - +
1611C BTN 5.7 2.2 - - - -
1620F PRO* 3.8 4.3 - - - -
1621F SER* 3.3 17.0 - - - -
1622F TYR 5.8 1.1 - - - -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 1.3 72.0 - - - +
21B HIS* 1.3 58.5 + - - +
23B VAL* 3.3 9.0 + - - +
24B GLN* 2.8 76.1 + - - +
61B TYR* 5.8 0.9 - - - +
65B ASP* 4.0 5.9 + - - -
20D GLN* 3.3 42.0 - - + +
24D GLN* 5.5 0.4 + - - -
204D UNX 4.0 9.4 + - - -
1620F PRO* 3.7 13.8 - - + +
1621F SER 2.9 20.4 + - - +
1623F SER* 3.7 8.7 - - - -
1626F SER* 4.2 1.7 - - - -
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Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.1 8.1 + - - +
20B GLN* 1.3 79.4 - - - +
22B SER* 1.3 60.5 + - - +
24B GLN* 4.3 4.2 - - - +
25B THR* 2.8 56.0 + - - +
1611C BTN 3.3 73.0 + + + +
1623F SER* 3.6 8.9 - - - +
1625F THR* 4.1 5.2 + - - -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU 4.2 1.7 + - - -
16B LEU* 3.5 11.0 - - - +
17B SER* 2.7 44.2 + - - -
19B SER* 2.8 21.9 + - - -
21B HIS* 1.3 77.4 - - - +
23B VAL* 1.3 63.7 + - - +
25B THR* 3.9 3.3 - - - -
26B LEU* 3.2 24.9 + - - +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.0 8.5 - - + -
17B SER 4.2 0.9 - - - +
19B SER 3.0 20.7 + - - +
20B GLN* 3.6 13.2 - - - +
22B SER* 1.3 78.0 - - - +
24B GLN* 1.3 57.8 + - + +
27B SER* 3.0 27.5 + - - -
58B THR* 4.0 31.0 - - + +
61B TYR* 3.8 23.6 - - + +
62B LEU* 3.7 14.9 - - - +
65B ASP* 3.9 15.5 - - + +
1620F PRO* 4.1 16.6 - - + -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 2.8 50.8 + - - +
21B HIS* 4.3 3.2 - - - +
23B VAL* 1.3 71.5 - - + +
25B THR* 1.3 64.7 + - - +
27B SER* 3.6 7.8 - - - -
28B LEU* 3.1 31.2 + - + +
65B ASP* 3.2 23.8 + - - +
69B ASN* 5.3 3.4 - - - +
1623F SER* 4.7 2.9 + - - -
1625F THR* 4.7 1.9 + - - +
1626F SER* 3.6 32.9 + - - +
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 2.8 45.7 + - - +
22B SER* 3.9 4.9 - - - -
24B GLN* 1.3 73.8 - - - +
26B LEU* 1.3 68.9 + - - +
28B LEU* 3.3 21.1 + - + +
29B TRP* 3.4 10.6 + - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.9 2.0 - - + -
12B LYS* 3.7 52.0 - - + +
13B LEU* 4.0 17.9 - - + +
16B LEU* 4.4 10.8 - - + -
22B SER 3.2 15.3 + - - +
23B VAL 4.0 2.9 - - - +
25B THR* 1.3 80.2 - - - +
27B SER* 1.3 63.6 + - - +
29B TRP* 3.0 28.6 + - + +
30B LEU* 3.1 21.7 + - + +
62B LEU* 3.7 28.0 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL 3.0 18.4 + - - -
24B GLN 3.6 3.6 - - - -
25B THR 3.3 0.2 - - - -
26B LEU* 1.3 76.3 - - - +
28B LEU* 1.3 61.1 + - - +
30B LEU* 3.4 3.3 + - - +
31B ILE* 3.0 31.6 + - - +
62B LEU* 4.0 3.7 - - - +
65B ASP* 2.6 34.5 + - - -
66B VAL* 3.5 32.7 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 3.1 22.0 + - + +
25B THR* 3.5 13.9 - - + +
26B LEU 3.2 0.2 - - - -
27B SER* 1.3 73.9 + - - +
29B TRP* 1.3 54.7 + - - +
31B ILE* 3.1 14.5 + - + +
32B HIS* 2.8 34.5 + - - +
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Residues in contact with TRP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.9 29.2 - + - -
5B SER 4.2 0.4 - - - -
8B ALA* 4.1 22.0 - - + -
9B LEU* 4.1 20.0 - - + -
12B LYS* 3.4 40.5 - - + +
25B THR 3.4 6.8 + - - +
26B LEU* 3.0 15.3 + - + +
28B LEU* 1.3 78.4 - - - +
30B LEU* 1.3 87.6 + - + +
32B HIS* 3.4 7.3 - - - +
33B HIS* 3.0 60.8 + + - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.6 30.7 - - + -
13B LEU* 5.7 0.9 - - + -
26B LEU* 3.1 30.0 + - + +
27B SER 3.7 5.6 - - - +
28B LEU 3.3 0.2 - - - -
29B TRP* 1.3 89.4 - - + +
31B ILE* 1.3 65.3 + - - +
33B HIS 3.2 4.8 + - - +
34B ARG 3.1 17.5 + - - -
40B ILE* 3.8 31.4 - - + -
44B TRP* 5.8 3.4 - - + -
62B LEU* 4.4 13.2 - - + -
66B VAL* 3.9 22.4 - - + -
77B PHE* 3.5 21.2 - - + -
81B PHE* 6.1 2.0 - - + -
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 3.0 34.0 + - - +
28B LEU* 3.1 13.7 + - + +
30B LEU* 1.3 72.6 - - - +
32B HIS* 1.3 67.3 + - - +
34B ARG* 2.9 45.9 + - - +
65B ASP* 5.0 0.2 - - - +
66B VAL* 4.3 18.2 - - + +
69B ASN* 3.5 39.5 - - + +
70B SER* 4.7 9.4 - - - -
73B LYS* 4.4 20.2 - - + +
77B PHE* 4.4 5.6 - - + -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 2.8 13.4 + - - +
29B TRP* 3.4 14.7 - - - +
31B ILE* 1.3 78.9 - - - +
33B HIS* 1.3 83.3 + + - +
34B ARG* 3.3 11.6 + - - +
35B LYS* 5.6 2.4 - - - +
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.5 47.7 + - + +
29B TRP* 3.0 63.6 + + + +
30B LEU* 3.2 6.7 + - - +
32B HIS* 1.3 102.2 + + - +
34B ARG* 1.3 54.4 + - - +
35B LYS* 3.1 6.7 - - - -
36B HIS* 2.9 34.1 + - + +
40B ILE* 3.4 8.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il